[phenixbb] special positions Refinement crash

Yarrow Madrona amadrona at uci.edu
Thu Oct 10 08:55:42 PDT 2013


Thank you Pavel,

Even setting this value up to 10 didn't seem to fix the issue. It seems to
crash. log report is below.


=========================== Add C-beta restraints
============================

Adding C-beta torsion restraints...
num c-beta restraints:  732

==================== Compute data/restraints target weights
===================

Traceback (most recent call last):
  File
"/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py",
line 159, in run
    call_back_handler=call_back_handler)
  File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py",
line 1593, in run
    reference_model_manager = self.reference_model_manager).result
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py",
line 171, in __init__
    ion_placement_manager = ion_placement_manager)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 87, in __init__
    self.call(self.weight,   "Compute data/restraints target weights")
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 137, in call
    func(prefix = prefix)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
line 302, in weight
    log         = self.log)
  File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py",
line 20, in run
    log                           = log)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 368, in __init__
    self.xyz_weights_result = self.xyz_weights()
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 411, in xyz_weights
    log=self.log)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
line 294, in __init__
    verbose=0)
  File
"/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py",
line 29, in shake_sites
    max_iterations = max_iterations))
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 43, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
line 259, in run
    log)
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
line 127, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 89, in compute_functional_and_gradients
    self.apply_shifts()
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
line 70, in apply_shifts
    site_cart=self.tmp.sites_shifted[i_seq])
  File
"/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py",
line 609, in correct_special_position
    raise AssertionError(error_message)
AssertionError: Excessive special position correction:
  unit_cell: (56.278, 67.256, 106.26, 90, 90, 90)
  space_group_info: P 21 2 2
  special_op: 1/2,y,1/2
  site_frac: (0.5155158345734757, 0.37698455671246006, 0.504900074345152)
  site_special_frac: (0.5, 0.37698455671246006, 0.5)
  distance_moved: 1.01666
udp021848uds:Refine_P2122 yarrowmadrona$

> Hi Yarrow,
>
> please try increasing this parameter (default is 1.0)
>
> correct_special_position_tolerance
>
> and let me know if this does not help. Set to 2 or so.
>
> Pavel
>
> On 10/9/13 4:17 PM, Yarrow Madrona wrote:
>> Hello,
>>
>> I am trying to do a refinement and I get an error that I think means I
>> have atoms on special positions. The refinement stops and gives the
>> following output given below. Any help would be appreciated. I am not
>> sure
>> how to exactly determine which atoms are at special positions.
>>
>> Thank you.
>>
>> -Yarrow
>>
>>
>> |-real space refinement
>> (target=simple)---------------------------------------|
>> | start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68
>> weight= 50|
>> | final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45
>> weight= 80|
>> |
>> ---------------------------------------------------------------------------
>> |
>>
>> ==================== Compute data/restraints target weights
>> ===================
>>
>> Traceback (most recent call last):
>>    File
>> "/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
>> line 11, in <module>
>>      command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py",
>> line 159, in run
>>      call_back_handler=call_back_handler)
>>    File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py",
>> line 1593, in run
>>      reference_model_manager = self.reference_model_manager).result
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py",
>> line 171, in __init__
>>      ion_placement_manager = ion_placement_manager)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
>> line 87, in __init__
>>      self.call(self.weight,   "Compute data/restraints target weights")
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
>> line 137, in call
>>      func(prefix = prefix)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
>> line 302, in weight
>>      log         = self.log)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py",
>> line 20, in run
>>      log                           = log)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
>> line 368, in __init__
>>      self.xyz_weights_result = self.xyz_weights()
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
>> line 411, in xyz_weights
>>      log=self.log)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
>> line 294, in __init__
>>      verbose=0)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py",
>> line 29, in shake_sites
>>      max_iterations = max_iterations))
>>    File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
>> line 43, in __init__
>>      exception_handling_params=lbfgs_exception_handling_params)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
>> line 259, in run
>>      log)
>>    File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
>> line 127, in run_c_plus_plus
>>      f, g = target_evaluator.compute_functional_and_gradients()
>>    File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
>> line 89, in compute_functional_and_gradients
>>      self.apply_shifts()
>>    File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
>> line 70, in apply_shifts
>>      site_cart=self.tmp.sites_shifted[i_seq])
>>    File
>> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py",
>> line 609, in correct_special_position
>>      raise AssertionError(error_message)
>> AssertionError: Excessive special position correction:
>>    unit_cell: (56.278, 67.256, 106.26, 90, 90, 90)
>>    space_group_info: P 21 2 2
>>    special_op: 1/2,y,1/2
>>    site_frac: (0.5090941495765681, 0.42722892547242985,
>> 0.5083083194012079)
>>    site_special_frac: (0.5, 0.42722892547242985, 0.5)
>>    distance_moved: 1.02047
>>
>> Phenix v. 1.8.4-1496
>>
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>


-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697




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